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Programming Language -Final Project- “Project 4”

Programming Language -Final Project- “Project 4”. 學生：林郁凱 謝侑娟 學號： 19709046 19709053 指導教師：鍾翊方 孫行人. Project 4: Identification of Monotonic Genes by H-test. Find all of ascending and descending Monotonic Genes

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Programming Language -Final Project- “Project 4”

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  1. Programming Language-Final Project-“Project 4” 學生：林郁凱 謝侑娟 學號：19709046 19709053 指導教師：鍾翊方 孫行人

  2. Project 4: Identification of Monotonic Genes by H-test • Find all of ascending and descending Monotonic Genes • For each gene, the mean of the gene expression values in each group is calculated. • Let the mean for gene i in group j be μij; j = 1,..., k, k is the number of groups. We sort μij in increasing (or decreasing) order. • If the order of the sorted μij is not the same as that of the unsorted μij, then we remove the gene from the list. • Perform H-test and rank genes by their H-value • Plot the results 2

  3. 1. Find all of ascending and descending Monotonic Genes a) mean of gene expression b) sort, increasing / decreasing order

  4. ESCN_Nor

  5. Increase (mean of expression)

  6. Ascending

  7. #Monotonic gene open (FILE, "ESCN_Nor.txt") || die "file open error!\n";$line_1=<FILE>;@monotonic=<FILE>;close(FILE); #分成5群(ESC EB d10 d17 NSC) @groups=(3, 3, 6, 6, 9); foreach (@monotonic){ @line_each=split(/\s+/,$_); $value_ref=[ [@line_each[1..3]], [@line_each[4..6]], [@line_each[7..12]], [@line_each[13..18]], [@line_each[19..27]] ];

  8. #求mean of gene expression for($i=0;$i<5;$i++){ for($d=0;$d< $groups[$i] ;$d++){ $num_1=$value_ref->[$i]->[$d]; $total_1+= $num_1; } $total_1=($total_1/$groups[$i]); $dd_1=$total_1; $total_1=();$num_1=(); push(@aa_1,$dd_1); } @cc_1=@aa_1; $dd_1=();@aa_1=(); unshift(@cc_1,$line_each[0]);

  9. #sorting (Ascending & Descending) for($t=1;$t<6;$t++){ if($cc_1[$t]>$cc_1[$t+1]){ $count2++; } } if($count2==1){ $strings1=join" ",@cc_1; push(@qq,$strings1); } elsif($count2==5){ $strings2=join" ",@cc_1; push(@rr,$strings2); } @cc_1=();$count2=(); * “undef”=0;

  10. foreach (@qq){ @line_increase=split(/\s+/,$_); $h_increase=$table{$line_increase[0]}; $table_increase->{$line_increase[0]} =$h_increase; } foreach (@rr){ @line_decrease=split(/\s+/,$_); $h_decrease=$table{$line_decrease[0]}; $table_decrease->{$line_decrease[0]} =$h_decrease; }

  11. 2. Perform H-test and rank genes by their H-value a)Kruskal-Wallis H test b)H-test (Modify~tied observations)

  12. H-test (Monotonic Genes) 12

  13. Ri= Ranks of a group Ni= samples of a group (ex:[ESC]~ 3 samples) C = groups (ex:[ESC EB d10 d17 NSC]~ 5 groups) N =total of samples (ex: [ESCN_Nor]~27 samples) Kruskal-Wallis H test

  14. probe_ID 「ESC . . EB . . D10 . . . . d17 . . . . . NSC . . . . . . . .」～ gene expression 排名(Rank)

  15. value frequency Repeat (value & frequency)

  16. 取中間值

  17. #將sample從大到小排序 for($u=1; $u<=$#line_each; $u++){ for($v=1; $v<=$#line_each; $v++){ if($line_each[$u] < $line_each[$v]){ $count++; } } $count=$count+1; push(@hh,$count); @h_test=@hh; $count=(); } @hh=(); probe_ID 「ESC . . EB . … D10 …. . . d17 . . NSC

  18. #找出重複的表現數值及頻率 foreach (@h_test){ if(exists $seen{$_}){ $seen{$_} += 1; } else{ $seen{$_} = 1; } } foreach $target (sort keys %seen){ $frequency= $seen{$target}; push(@targets,$target); push(@frequencys,$frequency); } %seen=();$target=();$frequency=(); @ties=@frequencys; value frequency

  19. #計算重複值的平均次序 (找中間值) for($g=0;$g<=$#targets;$g++){ $inter_value=$targets[$g]+ ($frequencys[$g]-1)/2; push(@inters,$inter_value); } @frequencys=();$inter_value=(); foreach (@h_test){ for($k=0;$k<=$#inters;$k++){ if($_ == $targets[$k]){ $_=" "; $_=~ s/(\s+)/$inters[$k]/; } } } @targets=();@inters=(); unshift(@h_test,$line_each[0]);

  20. ESC EB d10 d17 NSC 71 52 128 82 45 Ri值(1)

  21. ESC EB d10 d17 NSC Ri值(2)

  22. ESC EB d10 d17 NSC Ri平方

  23. $h_test_ref=[ [@h_test[1..3]], [@h_test[4..6]], [@h_test[7..12]], [@h_test[13..18]], [@h_test[19..27]] ];

  24. for($i=0;$i<5;$i++){ for($d=0;$d< $groups[$i] ;$d++){ $num_2=$h_test_ref->[$i]->[$d]; $total_2+= $num_2; } $dd_2=$total_2**2; $total_2=();$num_2=(); push(@aa_2,$dd_2); } @cc_2=@aa_2; $dd_2=();@aa_2=();

  25. Ri= Ranks of a group Ni= samples of a group (ex:[ESC]~ 3 samples) C = groups (ex:[ESC EB d10 d17 NSC]~ 5 groups) N =total of samples (ex: [ESCN_Nor]~27 samples) T = t3-t (t: tied observation, repeat frequency) H-test (Modify~tied observations)

  26. value frequency Repeat (value & frequency)

  27. # Kruskal-Wallis H test $sample=$#line_each; for($p=0; $p<=$#groups; $p++){ $series_numer=($cc_2[$p]/$groups[$p]); $all+= $series_numer; } for(@ties){ $series_denomin=($_**3 -$_); $repeat+= $series_denomin; } T = t3-t

  28. $h_numerator= (12/($sample*($sample+1)))*($all)-3*($sample+1) ; $h_denominator=1- ($repeat)/($sample**3 -$sample); $h=$h_numerator/$h_denominator; $h =sprintf "%.3f",$h; $table{$line_each[0]}=$h; $all=();$repeat=();$h_numerator=(); $h_denominator=();$h=(); }

  29. foreach (@qq){ @line_increase=split(/\s+/,$_); $h_increase=$table{$line_increase[0]}; $table_increase->{$line_increase[0]} =$h_increase; } foreach (@rr){ @line_decrease=split(/\s+/,$_); $h_decrease=$table{$line_decrease[0]}; $table_decrease->{$line_decrease[0]} =$h_decrease; }

  30. #Ascending/Descending H-test & Probe ID @results=qw/check_1 check_2/; @h_tables=($table_increase, $table_decrease); for($n=0; $n<=$#results; $n++){ $filename ="$results[$n].txt"; open(FILE, ">$results[$n].txt") || die"File open Error!\n"; foreach $item ( sort { $h_tables[$n]->{$b} <=> $h_tables[$n]->{$a} or $a <=> $b } keys %{$h_tables[$n]}) { $aa=$h_tables[$n]->{$item}; print FILE $item."\t".$aa."\n"; } print"已對檔案『$filename』寫出。\n"; close(FILE); } * Reference: $table_increase , $table_decrease

  31. Probe_ID H-value Ascending High value of H-test, gene express

  32. Probe_ID 「ESC . . EB . . d10 . . . . .」~gene expression Ascending Top 15 of H-test value, gene express

  33. #H-test of Ascending/Descending monotonic gene open (FILE, "check_1.txt") || die "file open error!\n"; @increase_h_test=<FILE>; close(FILE); open (FILE, "check_2.txt") || die "file open error!\n"; @decrease_h_test=<FILE>; close(FILE);

  34. #High value of H-test, for gene expression (Ascending & Descending) foreach (@increase_h_test){ @line1=split(/\s+/,$_); foreach(@check::monotonic){ if( $_=~/($line1[0](\s+)(.*))/){ push(@probes1,$1); push(@aa,@probes1); } @probes1=(); } } foreach (@decrease_h_test){ @line2=split(/\s+/,$_); foreach(@check::monotonic){ if( $_=~/($line2[0](\s+)(.*))/){ push(@probes2,$1); push(@bb,@probes2); } @probes2=(); } }

  35. #Top 15 of H-test value, for gene expression (Ascending & Descending) $filename ="top15_increase.txt"; open(FILE, ">top15_increase.txt")||die"File open Error!\n"; for($i=0; $i<15; $i++){ print FILE "$aa[$i]\n"; } print"已對檔案『$filename』寫出。\n"; close(FILE); $filename ="top15_decrease.txt"; open(FILE, ">top15_decrease.txt")||die"File open Error!\n"; for($i=0; $i<15; $i++){ print FILE "$bb[$i]\n"; } print"已對檔案『$filename』寫出。\n"; close(FILE);

  36. 3. Plot the results a) Setting “undef” b)GD::Graph

  37. Probe ID H_value Probe ID ESC EB d10 …... Top 5 of H-test value，Samples對Gene Expression values (Ascending)

  38. #Top 5 of H-test value，Samples對Gene Expression values @all=([@aa], [@bb]); @h_test=([@increase_h_test], [@decrease_h_test]); @name=qw/Image_top15_increase Image_top15_decrease/; for($s=0; $s<2; $s++){ for($m=0; $m<=14; $m++){ @line_each=split(/\s+/,$all[$s]->[$m]); @line3=split(/\s+/,$h_test[$s]->[$m]); $value_ref=[ [@line_each[1..3]], [@line_each[4..6]], [@line_each[7..12]], [@line_each[13..18]], [@line_each[19..27]] ];

  39. for($u=0; $u<27; $u++){ push(@re_undef,undef); } @line=@re_undef; @line_0=@line; @line_1=@line; @line_2=@line; @line_3=@line; @line_4=@line;

  40. for($u=0; $u<3; $u++){ $line_0[$u]= $line_each[$u+1]; } for($u=3; $u<6; $u++){ $line_1[$u]= $line_each[$u+1]; } for($u=6; $u<12; $u++){ $line_2[$u]= $line_each[$u+1]; } for($u=12; $u<18; $u++){ $line_3[$u]= $line_each[$u+1]; } for($u=18; $u<27; $u++){ $line_4[$u]= $line_each[$u+1]; } @re_undef=(); [1,2,3,un,un,un,un,un,un,un,un,un,un,un,un,un,un,…] [un,un,un,4,5,6,un,un,un,un,un,un,un,un,un,un,un,…] [un,un,un,un,un,un,7,8,9,10,11,12,un,un,un,un,un,…]

  41. use GD::Graph::points; @data=( [ undef ,undef , undef ,undef , 5 ,undef ,undef , undef , undef , 10 ,undef ,undef , undef ,undef, 15 ,undef , undef ,undef ,undef , 20 , undef , undef ,undef ,undef , 25 ,undef , undef], [@line_0],[@line_1],[@line_2], [@line_3],[@line_4], ); $chart= new GD::Graph::points(700,500); #長、寬

  42. $chart-> set( x_label => 'Samples', #x軸-標題 y_label => 'Gene Expression Values', #y軸-標題 title=> #主題 "$line_each[0] H_value:$line3[1]", marker_size => 2, #point大小 markers => [ 1 ], x_label_skip => 1, y_min_value => 0, box_axis => 0, x_min_value => 0, );

  43. @legend_keys= qw(ESC EB d10 d17 NSC); #point名稱 $chart-> set_legend(@legend_keys); $chart-> set( dclrs => [ qw(green pink blue yellow red) ] ); @line_each=(); $gd_object=$chart->plot(\@data); @data=(); @results=qw/image1 image2 image3 image4 image5 image6 image7 image8 image9 image10 image11 image12 image13 image14 image15/;

  44. $imagename = "$name[$s]/$results[$m].png"; open(IMAGE,">$name[$s]/ $results[$m].png") or die "open > $name[$s]/$results[$m].png: $!"; binmode IMAGE; print IMAGE $gd_object->png; print"已對檔案『$imagename』 寫出。\n"; close IMAGE; } }

  45. Probe ID H_value Probe ID ESC EB d10 …... Top 5 of H-test value，Samples對Gene Expression values (Ascending)

  46. Probe ID H_value Probe ID ESC EB d10 …... Top 5 of H-test value，Samples對Gene Expression values (Ascending)

  47. Probe ID H_value Probe ID ESC EB d10 …... Top 5 of H-test value，Samples對Gene Expression values (Ascending)

  48. Probe ID H_value Probe ID ESC EB d10 …... Top 5 of H-test value，Samples對Gene Expression values (Ascending)

  49. Thank you for listening!

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